Everything's Not Lost
by vinylcheese
Summary: Post COG. Clary and Jace think all is well, Valentines dead and they're finally together, well they have another thing coming.
1. Sometime Around Midnight

Prologue  
_And it starts, sometime around midnight..._

The young man stared out the window into the dark lengthened streets of New York. Although he knew he should be downstairs helping with dinner his thoughts were easily distracted by the beautiful night sky. It was on rare occasion that he'd gotten to see even one star with all the fossil fuels being burned daily, today however was different, everything was perfect. He sat for what felt like hours admiring the scene and awaiting the two figures to emerge in some form. The boy had assumed them to be driving in order to take the necessary boxes.  
He felt anxiety and stress wash over him as the first car in minutes began to slow to the curb below the seemingly empty church.  
His eyes were instantly drawn, staring intently as her body emerged from the passengers side. She was, figuratively of course, an angel gifted to him from the heavens, he knew he didn't deserve her and yet she loved him still, it only made her more amazing.  
She headed to the back of the car beginning to open the trunk, her mother coming to her aide, when he saw her body stiffen a tad. She felt as though she was being watched, thus, she turned her gaze to the only window on the front of the building still lit, a silhouette of the curly haired boy made her heart swell in her chest. They watched each other briefly until her mother pulled her out of her trance, stuffing a heavy box into her arms and tugging her along the steps and out of the boys curious gaze.  
By now the boys excitement and nervousness were scratching him from the inside out. He remembered he needed to keep himself calm, and with great difficulty he had managed to pull that off.  
Thinking of the endless kisses to come and the life they would now share with each other left a lingering image of her beauty in the back of the boys mind. He smiled to himself as he walked to greet her at the top of the elevator, heart rate increasing as the seconds ticked by.  
The doors opened and there stood the familiar goddess. It had been two weeks since the inseparable pair were forced to part, due to the preparation of this greater plan, yet after begging mercilessly their parents had reluctantly agreed.  
Her hair gave the illusion of an autumn maple resting softly against her shoulders awaiting his curious hands, he however was taking things at a slower pace, letting his eyes take in and memorize every piece of her. She did the same, wanting the strength of the moment to last forever. They continued that way for what he'd assumed to be an eternity before making the first move and stepping closer. He brought his hand up and caressed her cheek softly grabbing her hand with his other. She could feel the electricity running through the both of them as he angled his face closer to hers embracing her in a long and awaited kiss.  
Her body relaxed from the previously tensed position and she pulled her hand through his tangled blonde locks deepening their kiss, letting their tongues wrestle.  
He was the first to pull away, his arm still draped around her, gazing once again adoringly. His face broke into his trademark grin as he whispered clear enough for only her to hear.  
She smiled falling even more in love with the boy.  
"Welcome to your new home Clarissa Frey."

**Love it? Hate it? Lemme know :)**


	2. Linger

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Chapter One

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You've got me wrapped around your finger, do you have to let it linger...

"Guess who's back, back, back, back again? Alec's back tell a friend." He chanted as he pushed the large library doors open. He hadn't however expected an audience.  
"Well, looks like we've found the next white rapper. Slim Shady would be proud." Jace chuckled as he passed the shadow hunter in the hallway, Clary alongside him laughing.  
"Oh ha ha ha." He spat now taking a serious tone. "Well, you ready to be immersed in the wonderful world of demon killing Frey?"

This was Clary's first official day living at the institute. Maryse had decided it would be far better for Clary to start training as soon as possible. Jocelyn on the other hand was hesitant about the situation but gave in still uneasy about Clary knowing what she really was.  
"I still don't get why I can't unpack all my things first."

"Because, I'm running the show now and what I say goes." Alec could be such a power trip sometimes.  
"Just because Maryse and Robert aren't here doesn't mean-" Clary's voice was halted when Alec grabbed her arm and pulled her into the room after him. Jace just stood there smiling as she looked back.  
"Just have my girlfriend back in one piece Alec!"

_Girlfriend? _Clary blushed. That was something she could get used to. She watched Jace's face disappear behind the closing door.

Clary was sure all they'd be doing today was reading, covering basic rules and whatnot. She knew she would have to get it done sooner or later, she just preferred later.  
They both took a seat, Alec had already pulled the necessary books she was to read and memorize.  
"Well, before I let you physically harm yourself I'd rather you start of with some light reading."

_"Le Livre des Damnés"_ His accent perfect as he spoke the title. Who knew he was fluent in French.

"It contains literally everything you need to know in sorting out demons as well as greater demons. You should know this book like the back of your hand. All shadow hunters have read this book. Of course you'll be starting a little later."

She was hesitant before taking it.

Clary spent the next hour checking off the reading list with Alec, asking many questions along the way.

"The sooner you finish these the sooner Jace and I can bully you in the training room." A smile playing on his lips. Clary hadn't even thought of actually fighting Jace, her anxiousness grew thinking of how much more experienced he and Alec were.

The door to the library creaked open revealing a slender dark haired man looking dressed up with nowhere to go as usual.

"Well," he glanced at the clock above the desk in the corner then back to Magnus at the doorway. "I think we're done for now. You best have these finished within the next two weeks." His eyes were focused on Magnus while speaking to Clary.

She stood chuckling at the boys preoccupation, grabbing her books as Magnus strode over taking a seat next to Alec. Clary struggled at fitting all six heavy books in her hands.

"What are you trying to kill her?" Magnus' laughed watching her stagger to the door, books ready to topple onto the floor. Clary rolled her eyes.

"Thanks for everything Alec." She smiled grateful for his help in starting her off, he just waved an 'anytime' gesture focusing back on Magnus.

Clary had managed to make it all the way up to her new room dropping the books on the floor with a startling 'thunk'.

She peered around the naked room. The walls were bare, similar to Jace's room, boxes of Clary's clothes and various things were waiting to be unpacked and set up. Jocelyn had recently sold their apartment in order to return to the life she had left behind. She had moved into Luke's house, thus, Clary had brought majority of her things to the institute but left the rest with them. Only a desk and a bed, which she had slept in the previous night, were set up but none the less plain and simple.

"Enjoy some help unpacking miss?" A set of arms snaked their way around Clary's waist making her jump then relax into Jace's body. She surveyed the room once more.

"I could use some assistance." She smiled turning to face him, his arms still embracing her.

He smiled at the sight of her face. "You're beautiful, you know that right?" She blushed furiously before pecking him lightly on the lips, her hands coming up to wrap around his neck.

"I love you." She responded and she did so. Every moment with Jace felt perfect, lingering and timeless.

After a few minutes of unpacking boxes and sorting things, Clary noticed Jace had stopped. He was looking at something in one of the boxes, one of her old sketchbooks. She gently placed her folded shirts down and stood behind him and peering over his shoulder. She watched as he flipped through pictures of runes and demons carefully observing them until he came to one very familiar picture. His fingers gently brushed the sketch. It was amazing how she'd managed to capture his face in such detail, and by memory too. Jace felt as if he was staring in a mirror, a close up of his face lay smiling back at him on the paper.

She slowly pulled the sketch pad out of his hands a little embarrassed putting it on top of the desk with the others.

"Sorry, I didn't mean to be invasive." He bent down and continued pulling supplies out and placing them in drawers.

"It's alright, I don't mind." She smiled and helped him finish with the last couple boxes. It had taken them around an hour to complete and the room looked significantly cleaner, although the walls were still bare, Clary thought maybe she could put in some drapes over the single window or something to look more interesting.

Jace collapsed back onto the bed, hands behind his head and looking up to the ceiling. Clary followed, resting her head in the nook of his neck.

"You know" she started, "I think a Justin Bieber poster would look fantastic just above the bed."

"Who's that?" He reached and grabbed her hand with his.

"Oh never mind." She laughed glancing a dumbfounded Jace, making her giggle even harder. She guessed it was more of a 'mundane' thing.

He sighed brushing the comment off and rolled to face her pressing their foreheads together. Clary could tell that he was deep in thought, she smiled breathing in his scent and deciding to pull him out of his trance with a kiss. It was soft and innocent for the first few seconds before Clary deepened it challenging his tongue. The want intensified and Jace shifted his body so that he was suspended over her all while managing to keep the kiss. His right hand swept its way across her thigh making her shudder a little.

Their thoughts were both interrupted by the voice of Isabelle booming down the corridor.

"Dinner's Served!"

Clary groaned wanting to see just how far the moment would have taken them. She'd thought many times about taking it to the next level with Jace but this was a classic example as to why they hadn't managed.

Jace smiled a tad mischievously, his body still lingering above hers.

"Care for a sleepover tonight Miss Fray? It's invite only." Her heart rate quickened as she took in what he was implying. The seductive tone in his voice was enough to send her through the roof. She'd waited so long to finally have Jace to herself and this was her chance. The thought that his bedroom was right beside hers made Clary laugh internally.

"Possibly." She smiled gesturing him off her and towards the kitchen.

They were met there by Jace's siblings as well as Magnus, who's head was stuffed behind an In Style magazine.

"Oh, didn't realize Gandalf was staying for dinner." He smiled trying to get the warlocks panties in a bunch.

"I don't understand how you manage to put up with that thing Clary, although I must admit that one was creative." He chuckled still reading the article. Alec set a bowl of noodles onto the table and took a seat between Jace and Magnus, curious as to what his boyfriend was reading.

Izzy came forward with another bowl in hand, filled with tomato sauce and what Clary assumed to be meatballs.

"Don't worry," She took a seat beginning to dish up, "it's edible this time."

That was everyone's cue to start eating.

"So," Clary felt a little ill informed "when are Maryse and Robert returning?"

"Well mom left the day before last so she should be home tomorrow. Dad however has to stay in Alicante for some clave meeting. I think it has something to do with Jonathan's body not being recovered."

Clary glanced at Jace, his body more tense then before. She knew he felt at fault for letting Jonathan slip away like that. She sympathised for him, squeezing his hand from under the table, wishing she could relieve his pain.

Isabelle sensed the tension waves being given off by Jace and ended the subject.

"Magnus want to help me clean up?" She gestured to the mess around the dining room table.

"Not really, but how can I resist someone as cute as you." He smiled grabbing everyone's finished plates.

Once over, Clary had returned to her room in hopes of getting a little study time in for Alec's sake. She found herself becoming easily distracted with thoughts of Jace and the night to come as she began the demon's encyclopaedia. She found it incredibly boring, then again Clary was never one for books.

She dropped it onto the bed and went searching for Jace. She assumed him to be in his room but she was wrong. Clary lay on his bed taking in the only scent she couldn't get enough of. His bed seemed so much more comfortable and at home then hers for some reason.

"Well hello there. Care for an explanation to your breaking and entering." Jace joked closing the door behind him. He had just gotten out of the shower, wearing nothing but loosely fit boxers around his waist and carrying a towel. Clary saw the old scars from applying various runes over his torso.

"I was enjoying your bed. It's softer then mine." She tugged on the hem of his blanket.

He chuckled bringing the towel up to dry his curly blonde locks.

"Alec and I are going out hunting tomorrow night, it wont be long don't worry. Izzy wanted me to ask if you wanted to go out for dinner with her." Jace stated.

Clary felt like a liability, being stuck behind like a child.

'Oh, if Izzy wants to go with you it's alright I can stay here you know. I don't need to be babysat." She felt a tad defensive.

"Just letting you in on the plan. You and Izzy can discuss things, I have nothing to do with that." The smile returning to his face as he joined her, sitting on the edge of the bed.

She brought herself up beside him and he laid a gentle kiss on the her lips. Her arms snaked their way around his neck, entangling them in his hair. She deepened the kiss and Jace could tell she wanted more, hell he wanted the same thing.

"You know Clarissa," he mumbled between kisses "you're going to have to show me where we're taking this." He could feel her smile widen over his face and they suddenly broke apart.

"Oh I can show you all right." She laughed getting off him and locking the bedroom door.

"Clary, are you sure you want to do this?" His tone came serious now. "Because we don't have to do anything you don't want to."

"I love you Jace, if there's anything in this world I'm sure about it's you and you alone."

He came off the bed joining her at the door smiling, his face was enough to light up any room for Clary.

"Well I'm enjoying this sleepover already." His voice tempted her to fall into his arms. And she did just that too.

**I'm thinking of changing the rating to M... What about you folks?**


	3. And The Winner Is

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Chapter 2

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And Forever's not so long.

Clary awoke to Jace's body shifting beside her own. She wrapped her arms around his naked chest closing the gap between herself and Jace. He grabbed her hands with his, holding the two in place for awhile.

"Clary, Clary, Clary," he mumbled stroking her hands gently.

"Actually, my names Isabelle." Her figure lean against the now open bedroom door. Clary blushed violently and covered herself with blanket.

"It's okay children, nothing I haven't seen before. But uhm Jace, mom's home so I suggest getting your naked girlfriend out of your bed before hell ensues."

And that was all Jace needed to hear before launching off the bed and into his clothes on the floor within seconds. Izzy just laughed closing the door as she left. He picked Clary's clothes up and handed them to her, she tore them on quickly.

"It still smells like hot sex in here." Jace wiggled his eyebrow smiling.

"I better get out of here. Alec has me on a strict study schedule." Clary smiled. "I'm off to the library I guess. But I'll see you later?" Jace nodded kissing her gently on the lips. And with that she was off for a literary filled day.

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_

"Well look who we have here." Clary looked up from the heavy book to find Isabelle in full shadowhunting gear and taking a seat in the desk across the large library.

"Oh hey Izzy, didn't realize what time it was. What's up with the outfit? Are we still going out tonight?"

"Well, I'm really sorry Clary but there were these Harbane demons at the boardwalk on West street. It's been so long since I've been out and about." The regretful look on her face was replaced by a cunning smile. "Plus, your little sex buddy told me you didn't want me to baby-sit you anymore."

"Oh shut up!" Clary snapped at the girls taunt, Isabelle just laughed continuing to egg her on.

"OHHH CLARYYYY, BY THE ANGEL CLARY!" She moaned and laughed, her voice echoing through the hollow room.

"Your not being funny Izzy. Cut it out before I throw this book at your head!" She yelled furiously meeting Isabelle's irritating voice.

The library door creaked open with a bang and in flung a mess of inky hair much like Isabelle's.

"What in in god's name is going on in here!" Shouted Maryse. The two girls fell silent. Clary thought of how awkward the moment was and snickered sending laughter through Isabelle as well.

"Oh, it's only you two." A blow of relief washed over the woman when she realized the girls were alone. "What are you two-I don't even want to know," her hand flew up as to finish the conversation. "Just keep the noise level down, please." She eyed her daughter. "It's good to see your all settled in Clary." Maryse smiled at the girl before leaving.

"So you'll be okay to hang around here for awhile then? We should be back soon." Izzy lingered in the doorway.

"I'm fine Izzy, I can entertain myself." Clary went back to her reading.

The further Clary dived into the book the more boring and repetitive it became. Her head was now pounding heavily, and for that reason she left the book in the library in search of something to do.

She was a little upset Jace had gone without so much as a goodbye but didn't think much of it.

Maybe, she thought she could give Simon a call. It had been quite awhile since she'd spoke with him. She came to the institute knowing it would be difficult to keep in contact with her best friend, seeing as he could no longer enter the church.

She'd pulled out her cell phone when a loud knock sounded down the hallway. Pulled out of her thoughts she now paced down the corridor to answer the door. Clary thought by chance that it was Simon but surely he would have called before coming over.

She swung the door inward to find a deserted New York street. Now a little confused she took a step outside, looking for the person. Her heart picked up speed when she looked to her feet.

Her vision became limited and her breath shallow.

_Who did this?_ She stared petrified at the little brown box on the step.

_Okay Clary,_ She thought to herself, _get it together. There's nothing to be afraid of_.

She looked around one last time before running inside and slamming the door behind her.

Tears were threatening their way out Clary's eyes as she ran to find Maryse.

In the kitchen the woman looked up from the book she was reading, wondering what Clary was so tied up about.

"Maryse, someone left- I mean he was dead and-his hand and-" She let out a deep breath trying to relax herself.

"Jonathan was here."

**Sorry that was short. I also messed the chapter up a tad and had to re-upload it.**


	4. Teardrops

Chapter 3

_Teardrop on the fire_  
_Fearless on my breath..._

"I'm not getting a reading on any of it." Magnus said picking up Jonathans decapitated hand from the box.

The Morgenstern ring was placed on it's index finger, the same ring Clary had strung around her neck.

"I just don't understand." Luke paced the library. "It's like a crude prank or something."

The others had come back from the boardwalk immediately upon hearing the news. Jocelyn and Luke did the same.

"He must be toying with us, things like this don't just happen." Jace sat holding Clary's hand for comfort.

There was a long frustrated pause along the room. Finally Isabelle broke it.

"Well, what's our next plan then? What are we going to do about this, I mean if he knows we're here we aren't exactly safe, right?"

"Exactly. I've informed Robert on the news and he's taken it to the clave to discuss as well." said Maryse.

Luke nodded in understanding.

"As for you," he pointed at Clary on the couch. "We need you out of here. It's not safe for you nor is it safe for any one of us."

Clary rose her hand in protest but realized Luke was right. The others had far more training then her, they knew how to handle a situation like this.

"I will take you to Amatis's house. You'll stay there until we find out how the Clave is going to handle this situation. We'll leave tomorrow morning."

Clary nodded wanting to make things as easy as possible.

Everyone had went there separate ways but Jace and Clary sat in the same position. He held her hands in his for quite some time.

* * *

Clary lay in bed later that night reassuring herself the everything would be fine, even though she was to anxious to sleep. Thoughts of Jace wound inside her head when her door creaked open.

"Are you still awake?" He whispered coming closer to her bed. She sat up and looked at the time, 12:40.

"Want to come adventuring?" He already knew she'd say yes.

The two walked quietly to the greenhouse. Jace knew Clary adored the greenhouse, being the first kiss they had ever shared together it was sort of memorable.

"You're not coming with me are you? To Alicante I mean?" They stood by the window together.

"We still need to see what the Clave says but it's not looking like it. We need someone here if he comes back."

Clary wondered just how long she would have to go without seeing Jace. The thought twisted her stomach.

"It's going to be alright. We'll get him, we outnumber him." He could tell Clary wasn't getting any more relaxed by his words.

"Clary," he cupped her chin forcing her to look at him. "No one is going to hurt you. They will have to go through me first. I need you to know that I would die for you Clary, and I would do anything in my power to keep you safe."

She kept silent watching him, there was nothing to say back.

"I need you to promise me that you'll listen to Luke, God knows how obedient you are." He smiled trying to calm to situation down.

"Yes I will." She looked deeply into his eyes.

"This is only temporary. I'll call you every chance I can get." He smiled genuinely. "Plus, I've talked to Simon today, he was planning on coming over to Amatis's to for a visit. Company couldn't hurt."

Clary still found it weird, the newfound friendship between Simon and Jace. She was however still thrilled about seeing Simon for the first time in weeks. She missed there hang out days, eating junk food and playing _Halo 3. _

"Yeah, I could use some company." She smiled a little sadly looking at him still. "But I'll miss you."

Wrapping her hands around his waist she hugged him tightly. He held her to his chest.

"Don't worry, I'll be right here when it's all over."

Clary's eyelids became heavy, she let out a yawn.

"I best get you back to bed."

"No, I don't want you to go. Just a few more minutes." She tightened her grip on him a little wanting the moment to last as long as possible. She felt him chuckle lightly.

* * *

_"You're waiting for her." Clary could only see the back of Jace's figure standing in the grassy field._

_They were in Alicante, from what Clary could tell. The sky shining a bright blue and fields for miles._

_Jonathan nodded keeping the same calmness as Jace, staring off into the distance. Wind was blowing softly, letting the grass sway gently._

_Clary felt a high tension in the scene before her. She attempted to run, to call Jace's name out, but the words couldn't escape her lips._

_The boys didn't acknowledge Clary behind her, instead they stared at the figure now coming into view._

_The young girl looked to be about Clary's age. She was running toward them swiftly, long blonde waves trailing behind her. Jace started off toward her at a low jog, Jonathan still unmoving._

_The girl's arms outstretched as she collided with Jace, embracing him in a hug. She was half a head shorter then him making it easy for his lips to gently kiss her forehead._

_The time seemed to slow as Jonathan glanced behind him looking Clary directly in the eye, but Clary was already focused on the blade he was pulling out his belt._

_"No! No, no, no" She yelled, yet no sound came out._

_Her brother turned back and walked quickly to the duo, Jace's lips still on the girls brow. Jonathan placed one hand gently on the girls shoulder. His appearance now, much like Clary's, didn't seem to phase Jace or the blonde anymore._

_With one swift movement the blade struck forward straight through her heart and reaching Jace's body as well._

_She let out a cry of pain as blood spat out her chest. Jace continued to hold her tightly, trying not to let the pain phase him, trying to protect her._

_Clary fell to her knee's and sobbed._

_"I would die for you Audrey, I will do everything in my power to keep you safe." Jace's words came out choked as his shirt became soaked in dark crimson._

_All Clary could do was weep._

**DUH DUH DUH. Reviews on who this mystery girl is?**


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